From d46f46ff299bf46e62f2a8a6e24806eb639d2d7a Mon Sep 17 00:00:00 2001
From: Adrian Romberg <adrian.romberg@icloud.com>
Date: Mon, 9 Sep 2024 10:55:29 +0200
Subject: [PATCH 1/3] update readme

---
 README.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index b6cc799..484e86d 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,8 @@
 [![linting: pylint](https://img.shields.io/badge/linting-pylint-yellowgreen)](https://github.com/pylint-dev/pylint)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-<img src="/src/docs/img/logo.png" height="50%" width="50%">
+<img src="/docs/img/logo.png" height="50%" width="50%">
+
 <!-- start intro -->
 XspecT is a Python-based tool to taxonomically classify sequence-reads (or assembled genomes) on the species and/or sub-type level using [Bloom Filters] and a [Support Vector Machine]. It also identifies existing [blaOxa-genes] and provides a list of relevant research papers for further information.
 <br/><br/>
@@ -27,7 +28,7 @@ To install Xspect, please download the lastest 64 bit Python version and install
 ```
 pip install xspect
 ```
-Please note that Apple Silicon is currently not supported.
+Please note that Windows and Alpine Linux is currently not supported.
 
 ## Usage
 ### Get the Bloomfilters

From f08b16311d35fbc31b3bdbbe6476d245bcd96155 Mon Sep 17 00:00:00 2001
From: Adrian Romberg <adrian.romberg@icloud.com>
Date: Mon, 9 Sep 2024 11:00:04 +0200
Subject: [PATCH 2/3] ensure unique run names for parallel computing

---
 src/xspect/main.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/xspect/main.py b/src/xspect/main.py
index 2d2b33e..378ae34 100644
--- a/src/xspect/main.py
+++ b/src/xspect/main.py
@@ -2,6 +2,7 @@
 
 from pathlib import Path
 import datetime
+import uuid
 import click
 import uvicorn
 from xspect import fastapi
@@ -77,7 +78,7 @@ def classify(genus, path, meta, step):
     for idx, file_path in enumerate(file_paths):
         run = pipeline.run(file_path)
         time_str = datetime.datetime.now().strftime("%Y-%m-%d-%H-%M-%S")
-        save_path = get_xspect_runs_path() / f"run_{time_str}.json"
+        save_path = get_xspect_runs_path() / f"run_{time_str}_{uuid.uuid4()}.json"
         run.save(save_path)
         print(
             f"[{idx+1}/{len(file_paths)}] Run finished. Results saved to '{save_path}'."

From 2282b7f04b08f6808a4f0970a8d7b275244530ea Mon Sep 17 00:00:00 2001
From: Adrian Romberg <adrian.romberg@icloud.com>
Date: Mon, 9 Sep 2024 11:01:00 +0200
Subject: [PATCH 3/3] bump version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2740758..0849752 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "XspecT"
-version = "0.2.3"
+version = "0.2.4"
 description = "Tool to monitor and characterize pathogens using Bloom filters."
 readme = {file = "README.md", content-type = "text/markdown"}
 license = {file = "LICENSE"}